applications/staticProps/P2OrderParameter.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include "applications/staticProps/P2OrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

using namespace std;
namespace OpenMD {

  P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, 
                                     const string& sele1)
    : StaticAnalyser(info, filename), doVect_(true),
      selectionScript1_(sele1), evaluator1_(info), 
      evaluator2_(info), seleMan1_(info), seleMan2_(info) {
    
    setOutputName(getPrefix(filename) + ".p2");
    
    evaluator1_.loadScriptString(sele1);
    
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
  }

  P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, 
                                     const string& sele1, const string& sele2)
    : StaticAnalyser(info, filename), doVect_(false),
      selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), 
      evaluator2_(info), seleMan1_(info), seleMan2_(info) {
    
    setOutputName(getPrefix(filename) + ".p2");
    
    evaluator1_.loadScriptString(sele1);
    evaluator2_.loadScriptString(sele2);
    
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }else {
      sprintf( painCave.errMsg,
               "--sele1 must be static selection\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
    
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }else {
      sprintf( painCave.errMsg,
               "--sele2 must be static selection\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
    
    if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
      sprintf( painCave.errMsg,
               "The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
      
    }
    
    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;
    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
         sd1 != NULL && sd2 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {

      sdPairs_.push_back(make_pair(sd1, sd2));
    } 
  }

  void P2OrderParameter::process() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    StuntDouble* sd;
    int i, ii;
  
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();

    for (int i = 0; i < nFrames; i += step_) {
      reader.readFrame(i);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      
      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        //change the positions of atoms which belong to the rigidbodies
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }        
      }      

      Mat3x3d orderTensor(0.0);

      if (doVect_) {
        
        if  (evaluator1_.isDynamic()) 
          seleMan1_.setSelectionSet(evaluator1_.evaluate());
        
        for (sd = seleMan1_.beginSelected(ii); sd != NULL; 
             sd = seleMan1_.nextSelected(ii)) {
          if (sd->isDirectional()) {
            Vector3d vec = sd->getA().getColumn(2);
            vec.normalize();
            orderTensor += outProduct(vec, vec);
          }
        }
  
        orderTensor /= seleMan1_.getSelectionCount();

      } else {
            
        for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); 
             j != sdPairs_.end(); ++j) {
          Vector3d vec = j->first->getPos() - j->second->getPos();
          if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(vec);
          vec.normalize();
          orderTensor +=outProduct(vec, vec);
        }
      
        orderTensor /= sdPairs_.size();
      }
      

      orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();  
      
      Vector3d eigenvalues;
      Mat3x3d eigenvectors;    

      Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
      
      int which;
      RealType maxEval = 0.0;
      for(int k = 0; k< 3; k++){
        if(fabs(eigenvalues[k]) > maxEval){
          which = k;
          maxEval = fabs(eigenvalues[k]);
        }
      }
      RealType p2 = 1.5 * maxEval;
      
      //the eigen vector is already normalized in SquareMatrix3::diagonalize
      Vector3d director = eigenvectors.getColumn(which);
      if (director[0] < 0) {
        director.negate();
      }   

      RealType angle = 0.0;
      
      if (doVect_) {
        for (sd = seleMan1_.beginSelected(ii); sd != NULL; 
             sd = seleMan1_.nextSelected(ii)) {
          if (sd->isDirectional()) {
            Vector3d vec = sd->getA().getColumn(2);
            vec.normalize();
            angle += acos(dot(vec, director));
          }
        }
        angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0;
        
      } else {
        for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
          Vector3d vec = j->first->getPos() - j->second->getPos();
          if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(vec);
          vec.normalize();
          
          angle += acos(dot(vec, director)) ;
        }
        angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
      }

      OrderParam param;
      param.p2 = p2;
      param.director = director;
      param.angle = angle;

      orderParams_.push_back(param);       
    
    }
    
    writeP2();
    
  }

  void P2OrderParameter::writeP2() {

    ofstream os(getOutputFileName().c_str());
    os << "#radial distribution function\n";
    os<< "#selection1: (" << selectionScript1_ << ")\t";
    if (!doVect_) {
      os << "selection2: (" << selectionScript2_ << ")\n";
    }
    os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";    

    for (size_t i = 0; i < orderParams_.size(); ++i) {
      os <<  orderParams_[i].p2 << "\t"
         <<  orderParams_[i].director[0] << "\t"
         <<  orderParams_[i].director[1] << "\t"
         <<  orderParams_[i].director[2] << "\t"
         <<  orderParams_[i].angle << "\n";

    }

  }

}

Revision:	1543
Committed:	Tue Mar 15 20:55:16 2011 UTC (14 years, 1 month ago) by gezelter
File size:	8720 byte(s)
Log Message:	bug fix in P2
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "applications/staticProps/P2OrderParameter.hpp"
43	#include "utils/simError.h"
44	#include "io/DumpReader.hpp"
45	#include "primitives/Molecule.hpp"
46	#include "utils/NumericConstant.hpp"
47
48	using namespace std;
49	namespace OpenMD {
50
51	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
52	const string& sele1)
53	: StaticAnalyser(info, filename), doVect_(true),
54	selectionScript1_(sele1), evaluator1_(info),
55	evaluator2_(info), seleMan1_(info), seleMan2_(info) {
56
57	setOutputName(getPrefix(filename) + ".p2");
58
59	evaluator1_.loadScriptString(sele1);
60
61	if (!evaluator1_.isDynamic()) {
62	seleMan1_.setSelectionSet(evaluator1_.evaluate());
63	}
64	}
65
66	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
67	const string& sele1, const string& sele2)
68	: StaticAnalyser(info, filename), doVect_(false),
69	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info),
70	evaluator2_(info), seleMan1_(info), seleMan2_(info) {
71
72	setOutputName(getPrefix(filename) + ".p2");
73
74	evaluator1_.loadScriptString(sele1);
75	evaluator2_.loadScriptString(sele2);
76
77	if (!evaluator1_.isDynamic()) {
78	seleMan1_.setSelectionSet(evaluator1_.evaluate());
79	}else {
80	sprintf( painCave.errMsg,
81	"--sele1 must be static selection\n");
82	painCave.severity = OPENMD_ERROR;
83	painCave.isFatal = 1;
84	simError();
85	}
86
87	if (!evaluator2_.isDynamic()) {
88	seleMan2_.setSelectionSet(evaluator2_.evaluate());
89	}else {
90	sprintf( painCave.errMsg,
91	"--sele2 must be static selection\n");
92	painCave.severity = OPENMD_ERROR;
93	painCave.isFatal = 1;
94	simError();
95	}
96
97	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
98	sprintf( painCave.errMsg,
99	"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
100	painCave.severity = OPENMD_ERROR;
101	painCave.isFatal = 1;
102	simError();
103
104	}
105
106	int i;
107	int j;
108	StuntDouble* sd1;
109	StuntDouble* sd2;
110	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
111	sd1 != NULL && sd2 != NULL;
112	sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
113
114	sdPairs_.push_back(make_pair(sd1, sd2));
115	}
116	}
117
118	void P2OrderParameter::process() {
119	Molecule* mol;
120	RigidBody* rb;
121	SimInfo::MoleculeIterator mi;
122	Molecule::RigidBodyIterator rbIter;
123	StuntDouble* sd;
124	int i, ii;
125
126	DumpReader reader(info_, dumpFilename_);
127	int nFrames = reader.getNFrames();
128
129	for (int i = 0; i < nFrames; i += step_) {
130	reader.readFrame(i);
131	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
132
133	for (mol = info_->beginMolecule(mi); mol != NULL;
134	mol = info_->nextMolecule(mi)) {
135	//change the positions of atoms which belong to the rigidbodies
136	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
137	rb = mol->nextRigidBody(rbIter)) {
138	rb->updateAtoms();
139	}
140	}
141
142	Mat3x3d orderTensor(0.0);
143
144	if (doVect_) {
145
146	if (evaluator1_.isDynamic())
147	seleMan1_.setSelectionSet(evaluator1_.evaluate());
148
149	for (sd = seleMan1_.beginSelected(ii); sd != NULL;
150	sd = seleMan1_.nextSelected(ii)) {
151	if (sd->isDirectional()) {
152	Vector3d vec = sd->getA().getColumn(2);
153	vec.normalize();
154	orderTensor += outProduct(vec, vec);
155	}
156	}
157
158	orderTensor /= seleMan1_.getSelectionCount();
159
160	} else {
161
162	for (vector<pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin();
163	j != sdPairs_.end(); ++j) {
164	Vector3d vec = j->first->getPos() - j->second->getPos();
165	if (usePeriodicBoundaryConditions_)
166	currentSnapshot_->wrapVector(vec);
167	vec.normalize();
168	orderTensor +=outProduct(vec, vec);
169	}
170
171	orderTensor /= sdPairs_.size();
172	}
173
174
175	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
176
177	Vector3d eigenvalues;
178	Mat3x3d eigenvectors;
179
180	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
181
182	int which;
183	RealType maxEval = 0.0;
184	for(int k = 0; k< 3; k++){
185	if(fabs(eigenvalues[k]) > maxEval){
186	which = k;
187	maxEval = fabs(eigenvalues[k]);
188	}
189	}
190	RealType p2 = 1.5 * maxEval;
191
192	//the eigen vector is already normalized in SquareMatrix3::diagonalize
193	Vector3d director = eigenvectors.getColumn(which);
194	if (director[0] < 0) {
195	director.negate();
196	}
197
198	RealType angle = 0.0;
199
200	if (doVect_) {
201	for (sd = seleMan1_.beginSelected(ii); sd != NULL;
202	sd = seleMan1_.nextSelected(ii)) {
203	if (sd->isDirectional()) {
204	Vector3d vec = sd->getA().getColumn(2);
205	vec.normalize();
206	angle += acos(dot(vec, director));
207	}
208	}
209	angle = angle/(seleMan1_.getSelectionCount()NumericConstant::PI)180.0;
210
211	} else {
212	for (vector<pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
213	Vector3d vec = j->first->getPos() - j->second->getPos();
214	if (usePeriodicBoundaryConditions_)
215	currentSnapshot_->wrapVector(vec);
216	vec.normalize();
217
218	angle += acos(dot(vec, director)) ;
219	}
220	angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
221	}
222
223	OrderParam param;
224	param.p2 = p2;
225	param.director = director;
226	param.angle = angle;
227
228	orderParams_.push_back(param);
229
230	}
231
232	writeP2();
233
234	}
235
236	void P2OrderParameter::writeP2() {
237
238	ofstream os(getOutputFileName().c_str());
239	os << "#radial distribution function\n";
240	os<< "#selection1: (" << selectionScript1_ << ")\t";
241	if (!doVect_) {
242	os << "selection2: (" << selectionScript2_ << ")\n";
243	}
244	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
245
246	for (size_t i = 0; i < orderParams_.size(); ++i) {
247	os << orderParams_[i].p2 << "\t"
248	<< orderParams_[i].director[0] << "\t"
249	<< orderParams_[i].director[1] << "\t"
250	<< orderParams_[i].director[2] << "\t"
251	<< orderParams_[i].angle << "\n";
252
253	}
254
255	}
256
257	}
258